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Merge remote-tracking branch 'upstream/next' into enh/fs_long
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‎.circleci/config.yml‎

Lines changed: 31 additions & 90 deletions
Original file line numberDiff line numberDiff line change
@@ -83,32 +83,13 @@ _setup_fmriprep_docker: &setup_fmriprep_docker
8383
export PY3=$(pyenv versions | grep '3\.' |
8484
sed -e 's/.* 3\./3./' -e 's/ .*//')
8585
pyenv local $PY3
86-
mkdir -p /tmp/${DATASET}/derivatives
8786
pip install --upgrade pip
8887
pip install --upgrade /tmp/src/fmriprep/wrapper/
8988
9089
_check_outputs: &check_outputs
91-
name: Checking outputs of fMRIPrep run
90+
name: Show outputs of fMRIPrep run
9291
command: |
93-
set +e -x
94-
mkdir -p /tmp/${DATASET}/test
95-
find /tmp/${DATASET}/${SUBDIR:-derivatives} \( -path '*/figures' -o -path '*/log' -o -path '*/sourcedata' \) -prune -o -name "*" -print | cut -d/ -f 5- | sort > /tmp/${DATASET}/test/outputs.out
96-
97-
FASTTRACK_OUTPUTS="${DATASET}${VARIANT}_fasttrack_outputs.txt"
98-
FULL_OUTPUTS="${DATASET}${VARIANT}_outputs.txt"
99-
RET=1
100-
if [ ! -f /tmp/.nofasttrack ]; then
101-
echo "Checking fasttrack..."
102-
diff /tmp/src/fmriprep/.circleci/${FASTTRACK_OUTPUTS} /tmp/${DATASET}/test/outputs.out
103-
RET=$?
104-
fi
105-
if [ $RET -ne 0 ]; then
106-
echo "Checking full..."
107-
diff /tmp/src/fmriprep/.circleci/${FULL_OUTPUTS} /tmp/${DATASET}/test/outputs.out
108-
RET=$?
109-
fi
110-
exit $RET
111-
92+
find /tmp/${DATASET}/${SUBDIR:-fmriprep} \( -path '*/figures' -o -path '*/log' -o -path '*/sourcedata' \) -prune -o -name "*" -print | cut -d/ -f 5- | sort
11293
11394
version: 2.1
11495
aliases:
@@ -455,14 +436,13 @@ jobs:
455436
name: Run anatomical workflow on ds005
456437
no_output_timeout: 2h
457438
command: |
458-
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/derivatives
439+
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/fmriprep
459440
if [ -f /tmp/.nofasttrack ]; then
460441
fmriprep-docker -i nipreps/fmriprep:latest \
461442
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
462443
--network none \
463444
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
464-
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
465-
--output-layout legacy \
445+
/tmp/data/${DATASET} /tmp/${DATASET}/fmriprep participant \
466446
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
467447
--skull-strip-template OASIS30ANTs:res-1 \
468448
--output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \
@@ -474,7 +454,7 @@ jobs:
474454
command: |
475455
rm -rf /tmp/${DATASET}/work/fmriprep_*_wf/fsdir*
476456
rm -rf /tmp/${DATASET}/work/reportlets
477-
rm -rf /tmp/${DATASET}/derivatives/fmriprep
457+
rm -rf /tmp/${DATASET}/fmriprep
478458
- save_cache:
479459
key: ds005-anat-v0-{{ .Branch }}-{{ .Revision }}
480460
paths:
@@ -488,7 +468,7 @@ jobs:
488468
name: Run full fMRIPrep on ds005 (LegacyMultiProc plugin)
489469
no_output_timeout: 2h
490470
command: |
491-
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep"
471+
FASTRACK_ARG="--derivatives anat=/tmp/${DATASET}/smriprep"
492472
if [ -f /tmp/.nofasttrack ]; then
493473
FASTRACK_ARG=""
494474
fi
@@ -502,89 +482,54 @@ jobs:
502482
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
503483
--network none \
504484
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
505-
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
485+
/tmp/data/${DATASET} /tmp/${DATASET}/fmriprep participant \
506486
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
507487
${FASTRACK_ARG} \
508-
--output-layout legacy \
509488
--sloppy --write-graph --mem-mb 14336 \
510489
--skull-strip-template OASIS30ANTs:res-1 \
511490
--output-spaces fsaverage5 fsnative \
512491
--use-plugin /tmp/src/fmriprep/.circleci/legacy.yml \
513492
--nthreads 4 -vv
514493
- store_artifacts:
515-
path: /tmp/ds005/derivatives
494+
path: /tmp/ds005/fmriprep
516495
destination: full-run
517496
- run:
518497
name: Copy intermediate results for re-runs
519498
command: |
520-
mkdir -p /tmp/${DATASET}/derivatives_partial
499+
mkdir -p /tmp/${DATASET}/fmriprep-partial
521500
sudo cp -a /tmp/${DATASET}/work /tmp/${DATASET}/work_partial
522501
sudo cp -a /tmp/${DATASET}/work /tmp/${DATASET}/work_bids
523502
# Nipype sometimes fails to pick up when the base directory changes
524503
# This is a cheap workflow, so let's not fuss
525504
sudo rm -rf /tmp/${DATASET}/work /tmp/${DATASET}/work_bids/fmriprep_*_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf || true
526-
- run:
527-
<<: *check_outputs
528-
environment:
529-
VARIANT: '_legacy'
530-
- run:
531-
name: Prepare BIDS Derivatives dataset
532-
command: |
533-
mkdir -p /tmp/${DATASET}/bids/sourcedata
534-
cp -r /tmp/${DATASET}/freesurfer /tmp/${DATASET}/bids/sourcedata/freesurfer
535-
- run:
536-
name: Re-run with BIDS layout
537-
no_output_timeout: 2h
538-
command: |
539-
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep"
540-
if [ -f /tmp/.nofasttrack ]; then
541-
FASTRACK_ARG=""
542-
fi
543-
fmriprep-docker -i nipreps/fmriprep:latest \
544-
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
545-
--network none \
546-
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work_bids \
547-
/tmp/data/${DATASET}/ /tmp/${DATASET}/bids participant \
548-
${FASTRACK_ARG} \
549-
--sloppy --write-graph --mem-mb 14336 \
550-
--output-spaces fsaverage5 \
551-
--nthreads 4 -vv
552-
- store_artifacts:
553-
path: /tmp/ds005/bids
554-
destination: bids-run
555-
- run:
556-
<<: *check_outputs
557-
environment:
558-
VARIANT: '_bids'
559-
SUBDIR: 'bids'
505+
- run: *check_outputs
560506
- run:
561507
name: Re-run fMRIPrep on single run of task data
562508
no_output_timeout: 2h
563509
command: |
564510
rm /tmp/data/${DATASET}/sub-01/func/*_run-01_*
565-
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep"
511+
FASTRACK_ARG="--derivatives anat=/tmp/${DATASET}/smriprep"
566512
if [ -f /tmp/.nofasttrack ]; then
567513
FASTRACK_ARG=""
568514
fi
569515
fmriprep-docker -i nipreps/fmriprep:latest \
570516
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
571517
--network none \
572518
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work_partial \
573-
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives_partial participant \
519+
/tmp/data/${DATASET} /tmp/${DATASET}/fmriprep-partial participant \
574520
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
575521
${FASTRACK_ARG} \
576-
--output-layout legacy \
577522
--sloppy --write-graph --use-syn-sdc --mem-mb 14336 \
578523
--output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
579524
--nthreads 4 --cifti-output --project-goodvoxels -vv
580525
- store_artifacts:
581-
path: /tmp/ds005/derivatives_partial
526+
path: /tmp/ds005/fmriprep-partial
582527
destination: partial-run
583528
- run:
584529
<<: *check_outputs
585530
environment:
586-
VARIANT: '_legacy_partial'
587-
SUBDIR: 'derivatives_partial'
531+
VARIANT: '_partial'
532+
SUBDIR: 'fmriprep-partial'
588533
- run:
589534
name: Clean working directory
590535
when: on_success
@@ -643,13 +588,12 @@ jobs:
643588
name: Run anatomical workflow on ds054
644589
no_output_timeout: 2h
645590
command: |
646-
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/derivatives
591+
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/fmriprep
647592
if [ -f /tmp/.nofasttrack ]; then
648593
fmriprep-docker -i nipreps/fmriprep:latest \
649594
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
650595
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
651-
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
652-
--output-layout legacy \
596+
/tmp/data/${DATASET} /tmp/${DATASET}/fmriprep participant \
653597
--fs-no-reconall --sloppy --write-graph \
654598
--output-spaces MNI152NLin2009cAsym \
655599
--mem-mb 14336 --nthreads 4 --anat-only -vv
@@ -659,7 +603,7 @@ jobs:
659603
command: |
660604
rm -rf /tmp/${DATASET}/work/fmriprep_*_wf/fsdir*
661605
rm -rf /tmp/${DATASET}/work/reportlets
662-
rm -rf /tmp/${DATASET}/derivatives/fmriprep
606+
rm -rf /tmp/${DATASET}/fmriprep
663607
- save_cache:
664608
key: ds054-anat-v0-{{ .Branch }}-{{ .Revision }}
665609
paths:
@@ -669,16 +613,15 @@ jobs:
669613
name: Run full fMRIPrep on ds054
670614
no_output_timeout: 2h
671615
command: |
672-
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep"
616+
FASTRACK_ARG="--derivatives anat=/tmp/${DATASET}/smriprep"
673617
if [ -f /tmp/.nofasttrack ]; then
674618
FASTRACK_ARG=""
675619
fi
676620
fmriprep-docker -i nipreps/fmriprep:latest \
677621
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
678622
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
679-
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
623+
/tmp/data/${DATASET} /tmp/${DATASET}/fmriprep participant \
680624
${FASTRACK_ARG} \
681-
--output-layout legacy \
682625
--fs-no-reconall --sloppy \
683626
--output-spaces MNI152NLin2009cAsym:res-2 anat func \
684627
--mem-mb 14336 --nthreads 4 -vv --debug compcor
@@ -687,18 +630,17 @@ jobs:
687630
name: Generate report with one artificial error
688631
command: |
689632
set -x
690-
sudo mv /tmp/${DATASET}/derivatives/fmriprep/sub-100185.html \
691-
/tmp/${DATASET}/derivatives/fmriprep/sub-100185_noerror.html
633+
sudo mv /tmp/${DATASET}/fmriprep/sub-100185.html \
634+
/tmp/${DATASET}/fmriprep/sub-100185_noerror.html
692635
UUID=$(grep uuid /tmp/${DATASET}/work/*/config.toml | cut -d\" -f 2 | tail -n 1)
693-
mkdir -p /tmp/${DATASET}/derivatives/fmriprep/sub-100185/log/$UUID/
636+
mkdir -p /tmp/${DATASET}/fmriprep/sub-100185/log/$UUID/
694637
cp /tmp/src/fmriprep/fmriprep/data/tests/crash_files/*.txt \
695-
/tmp/${DATASET}/derivatives/fmriprep/sub-100185/log/$UUID/
638+
/tmp/${DATASET}/fmriprep/sub-100185/log/$UUID/
696639
set +e
697640
fmriprep-docker -i nipreps/fmriprep:latest \
698641
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
699642
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
700-
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
701-
--output-layout legacy \
643+
/tmp/data/${DATASET} /tmp/${DATASET}/fmriprep participant \
702644
--fs-no-reconall --sloppy --write-graph \
703645
--output-spaces MNI152NLin2009cAsym:res-2 anat func \
704646
--reports-only --config-file /tmp/${DATASET}/work/${UUID}/config.toml -vv
@@ -759,13 +701,12 @@ jobs:
759701
name: Run anatomical workflow on ds000210
760702
no_output_timeout: 2h
761703
command: |
762-
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/derivatives
704+
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/fmriprep
763705
if [ -f /tmp/.nofasttrack ]; then
764706
fmriprep-docker -i nipreps/fmriprep:latest \
765707
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
766708
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
767-
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
768-
--output-layout legacy \
709+
/tmp/data/${DATASET} /tmp/${DATASET}/fmriprep participant \
769710
--fs-no-reconall --sloppy --write-graph \
770711
--output-spaces MNI152NLin2009cAsym \
771712
--mem-mb 14336 --nthreads 4 --anat-only -vv --notrack
@@ -775,7 +716,7 @@ jobs:
775716
command: |
776717
rm -rf /tmp/${DATASET}/work/fmriprep_*_wf/fsdir*
777718
rm -rf /tmp/${DATASET}/work/reportlets
778-
rm -rf /tmp/${DATASET}/derivatives/fmriprep
719+
rm -rf /tmp/${DATASET}/fmriprep
779720
- save_cache:
780721
key: ds210-anat-v1-{{ .Branch }}-{{ .Revision }}
781722
paths:
@@ -791,7 +732,7 @@ jobs:
791732
name: Run full fMRIPrep on ds000210
792733
no_output_timeout: 2h
793734
command: |
794-
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep"
735+
FASTRACK_ARG="--derivatives anat=/tmp/${DATASET}/smriprep"
795736
if [ -f /tmp/.nofasttrack ]; then
796737
FASTRACK_ARG=""
797738
fi
@@ -805,9 +746,9 @@ jobs:
805746
fmriprep-docker -i nipreps/fmriprep:latest \
806747
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
807748
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
808-
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
749+
/tmp/data/${DATASET} /tmp/${DATASET}/fmriprep participant \
809750
${FASTRACK_ARG} \
810-
--output-layout legacy --me-output-echos \
751+
--me-output-echos \
811752
--fs-no-reconall --use-syn-sdc --ignore slicetiming \
812753
--dummy-scans 1 --sloppy --write-graph \
813754
--output-spaces MNI152NLin2009cAsym \

‎.circleci/ds005_bids_fasttrack_outputs.txt‎

Lines changed: 0 additions & 33 deletions
This file was deleted.

‎.circleci/ds005_legacy_fasttrack_outputs.txt‎

Lines changed: 0 additions & 42 deletions
This file was deleted.

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